Legends to Supplementary Figures

Figure S1. The characteristics of the peptide anchor residues place Patr-AL in the A02 supertype. The anchor

residues found for Patr-AL in this study are shown at the top. Anchor residues reported in the SYFPETHI database for

other HLA-A and Patr-A allotypes are grouped by their supertype designation (Sidney et al). U denotes unclassified

supertype. Anchor residues are in bold and auxillary anchors in italics. Identities with anchor and auxiliary anchor

residues of Patr-AL are given in red and blue, respectively. The residues at positions 9 and 116 of the MHC sequence are

shown to the right.

Figure S2. Amino acid sequences of peptides bound to Patr-AL, HLA-A*0201, and HLA-A*0207. Protein of origin and GenBank accession number are shown for each peptide. Anchor residues are boldened.

Figure S3. Alignment of the amino-acid sequences of Patr-AL, HLA-A*0201, and HLA-A*0207. The leader peptide is not included. Domain boundaries are indicated by short vertical lines above the Patr-AL sequence. Patr-AL EAL-2 is the most common allele and was used for the structure determination.

Figure S4. Stereoscopic view of electron density around the peptide ALDKATVLL contoured at 1. Peptide is colored by B-factor on a scale from 20 to 50 Å2 (blue to red).

Figure S5. Details of the allotypes and peptides compared in Figure 4E. For comparison of peptide conformation,

residues 1-180 of Patr-AL were aligned using PyMOL to the following structures (Protein Data Bank ID

indicated in brackets): HLA-A*0201-LLFGYPVYV (1HHK), HLA-A*0201 FLWGPRALV (1QEW), HLA-

A*0201 ALWGFFPVL (1B0G), HLA-A*0201 GILGFVFTL (1HHI), HLA-A*0201 TLTSCNTSV (1HHG),

HLA-B*4401 (1SYV), HLA-B*4403 (1SYS), HLA-A*0101 (1W72), HLA-A*0201 (1HHJ), HLA-B*5301

(1A1O), HLA-C*0401 (1QQD), HLA-B*2705 (1A83), HLA-B*3501 (2CIK), HLA-E*0101 (1MHE), HLA-

B*1501 (1XR9), HLA-Cw*0301 (1EFX), HLA-G*0101 (2D31), HLA-B*0801 (1M05), HLA-A*1101 (2HN7),

1 HLA-A*1101 (1X7Q), HLA-A*2402 (2BCK). Root mean-square distances between Ca carbons of peptides in

different structures were measured in PyMOL.

Figure S6. Phylogenetic analysis of the gene segment beginning 300bp upstream of the ATG start codon and ending in exon 2 for MHC-A and –AL. Phylogenetic reconstruction was performed using neighbor-joining, maximum-

likelihood, and maximum-parsimony methods. Shown is the maximum likelihood tree, with midpoint rooting and black,

grey and white circles indicating 180, 60 and 50% bootstrap support, respectively, with all three methods. For four nodes

where one of the three methods had support of <50% the values for the remaining methods are shown (from top to

bottom: neighbor-joining, parsimony, and maximum likelihood).The node support was omitted for the nodes not supported by at least two methods with values 150%.

2 Supplemental figure S1

Peptide residue MHC residue supertype allotype 1 2 3 4 5 6 7 8 9 (C-term) 9 116 Patr AL LQVMI D LV IFA FY HLA-A*0201 LM V VL FY HLA-A*0202 LV L FY HLA-A*0204 LLFY HLA-A*0205 V L IMQ VLA L YY A02 HLA-A*0206 V V YY HLA-A*0207 L D L FY HLA-A*0214 VQL LVF L YY HLA-A*0217 L P L FY HLA-A*6802 T V VL YY HLA-A*6901 VTA IFLM IFL VL YY HLA-A*24 Y IV F ILF SY HLA-A*2402 YF LFI SY A24 Patr-A*0701 YFMLI VLMAFI SL Patr-A*0901 WYF MLIVA SY HLA-A*01 TS DE L Y FD HLA-A*3002 YFLV Y SH HLA-A*3003 FYIVL Y SH A01 HLA-A*3004 V YT QMIF YML SH HLA-A*2601 VTILF ILV YF YD HLA-A*2602 VTILF ILV YF YN HLA-A*2603 E VTILF FILVY YFML YD HLA-A*03 LVM FY IMFVL ILMF KYF FD HLA-A*1101 VI FY MLFYIA LIYVF KR YD HLA-A*3101 L V YF FLYW LFVI R TD HLA-A*3303 A I L FY V R TD HLA-A*6601 ED TV RK YD A03 HLA-A*6602 S VTRYD HLA-A*6603 S VTRYD HLA-A*6801 DE VTRKYD Patr-A*0101 FMLI RK FD Patr-A*0301 ASTG IV RKY YD A01 A03 HLA-A*3001 YF L SH A01 A24 HLA-A*2902 E F Y TD U Patr-A*0401 HKRACMSY YFMRW RK SD U Patr-A*0602 ANSQT P LIVM Y SD Supplemental figure S2

Accession # Protein Description A*0201 A*0207 Patr-AL P1 P2 P3 P4 P5 P6 P7 P8 P9 P10 P11 CT P61769 β2-microglobulin Y V DDTQFVRF F NM_001080856 Hypothetical protein LOC729164 L L MSFSVCL L P69905 Hemoglobin-α S L DKFLANV V P06733 α-enolase F I KDYPVVS I I NM_000429 Methionine adenosyltransferase Y L DEDT I YHL L P00558 Phosphoglycerate kinase S L EPVAVEL L P14174 Macrophage migration inhibitory factor F L SELTQQL L P05388 Ribosomal protein P0 F L ADPSAFVAAA P61604 HSP10 V L DDKDYF L L AAC50116 RAK kinase T E ADKSTV I I P04844 Ribophorin II R L DELGGVYL L NM_002343 Transferrin Y L GDDYVRAM M EAW82246 Gasdermin domain-containing 1 V I DSDLDVLL L AAS00488 Migration-inducing gene 10 protein F L A I LGGAKV V NP_009191 Lysophospholipase II F L EKLLPPV V AAS00488 Migration-inducing gene 10 protein V L PGVDALSN I I NP_003519 Histone 2B F V ND I FER I I NP_631898 Dipeptidylpeptidase 9 F L DENVHFF F P49406 Mitochondrial ribosomal protein L19 R L DDSL LYL L P35602 AP-1 complex subunit μ A I VDKVPSV V AAD47141 ABC Transporter L L DEPTNHL L Q9NYB9 Abl interactor 2 I L DD I GHGV V AAR16191 MLAA-42 antigen I L TD I TKGV V Q969V6 MKL1 Protein F L DGHDLQL L NP_002113 MHC Class II DQα F I IQGLRSV V P83876 Spliceosomal protein DIM1 K M DEVLYS I I BAA02430 Dipeptidase precursor K V ASL I GV V BAA34511 KIAA0791 prot ein A V DG I SLHL L P13796 L-plastin A L PEDLVEV V EAW95142 Chloride intracellular channel 4 F L DGNEMT L L NP_116231 Hypothetical protein FLJ14803 Y L FER I KEL L P62906 Ribosomal protein L10a F L ASESL I KQ I I AAD47141 ABC Transporter F L DEPTNHL L P84098 Ribosomal protein L19 I L MEH I HKL L BAD02827 Cytochrome P450 M K HLPGPQ Q Q96QK1 Vacuolar sorting protein VPS35 V M APHEPLV V P84098 Ribosomal protein L19 L M EH I HKL L NP_006806 Coated vesicle membrane protein K M GL I FEV V AAH09524 PSMD14 protein F V DDYTVRV V Q9BYN0 Sulfiredoxin-1 T L SDLRVYL L Q4KMQ2 Transmembrane protein 16F V L DDKLVFV V O43818 U3 snoRNP protein 3 A L LDKLYAL L O75460 IRE1 kinase precursor T L DGSLHAV V CAG29343 Ras-related RAN A Q YEHDLEV V AAH29387 Hemoglobin, γ-G H L DDLKGTFA A P00558 Phosphoglycerate kinase A L MDEVVKA A P50579 Methionine aminopeptidase 2 A Q FEHT I LL L P00338 Lactate dehydrogenase variant A G L YG I KDDVF L L Q13151 Ribosomal protein A0 A V DGNTVEL L NP_006754 B cell translocation gene 2 K M DP I I SRV V P13639 eEF2 K M DRAL LEL L P08708 Ribosomal protein S17 A L DQE I I EV V EAW79040 Coatomer protein complex subunit β2 H L DRTMYL L L CAI14173 Chaperonin CCT3 A L DDM I ST L L Q02809 Lysyl hydroxylase 1 A L DEVVLKF F Q99567 Numan nucleoporin 88 I L DPHVVLL L NP_031399 Human suppressor of clear homolog (SOC-2) R L DSLTTLYL L P19237 Troponin I Y L AER I PTL L CAA60786 Proteasome subunit LMP7 K V IENPYL L P42696 RNA-binding protein 34 V L FENTDSVHLV CAG38481 DSIPI p ro t ein S L LGGDVVSV V Q92621 Nucleoporin NUP205 A L LDR I VSV V Q04637 eIF4g V L MTED I KL L P14174 Macrophage migration inhibitory factor F L SELTQQLA A BAA95563 TRP channel-related 7 R V ADV I AQV V P11216 Glycogen phosphorylase N L AEN I SRV V CAA88733 Helicase Y L DQT L PRA A CAI13665 GTP-binding protein 4 T L TEEGVI KV V P14923 Junction plakoglobin N L MEQP I KV V NP_057146 Hypothetical protein LOC51647 T L IGLSIKV V P20591 Interferon-induced protein Mx T L IDLPGITRVV P04035 HMG-CoA Reductase F L DKELTGL L AAG44629 Dendritic cell protein DC23 I I DGVKVQV V NP_008835 DNA-PK L L DENNVSSYLL AAB58363 Lysyl hydroxylase isoform 2 A VDEVVLKF F EAW97938 Serine/threonine phosphatase 1, γ subunit N IDSI IQRL L P49720 Proteasome subunit beta type 3 H LFET I SQA A AAH32618 Ring finger protein 20 H LDEARTLL L AAG00606 RP42 protein A LDPAS I SV V NP_002255 Karyopherin alpha S VDDIVKGI I AAH56687 Cancer antigen SDCCAG1 A VDEFYSK I I Q92538 Golgi brefeldin resistance factor 1 F VDPNGK I SL L P04406 Glyceraldehyde-3-phoshphate dehydrogenase G LMTTVHAI I NP_006707 Activator of S-phase kinase V VDDIVSKL L CAI95003 KIAA1432 prot ein N LDNAFAHV V P04406 Glyceraldehyde-3-phoshphate dehydrogenase G LMTTVHAI TAA NP_037471 Asparagine-linked glycosylation 6 K LPD[ IL]FSVV AAG44629 PHD finger-containing 11 L LPTGVFQV V AAP74806 Proliferation inducing gene 5 L LDGVVEKL L Q5SW96 LDLR adaptor protein 1 G LDEAFSRL L AAB37682 GCN5L1 protein L VDHLNVGV V Q9BV68 RING finger protein 126 G LDAI ITQL L Q92786 Homeobox prospero-like PROX1 A LDKH I LGF F Q9P2M7 Cingulin A QDPTMLQF F Q9NRL3 Zinedin A VDPNGAFLM M Q13588 GRB2-related adapter protein A QDPSQLSF F P23771 Transcription factor GATA-3 A QYPLPEEV V NP_055271 Programmed cell death 4 A LDKATVLL L AAH48261 Kinase CDC42BPB A LQKE I LML L CAG33546 Trimethyllysine hydroxylase epsilon R LDETTLFF F AAH14143 Histone acetyltransferase MYST4 V QDGSVLKV V AAH42999 ASXL2 protein R QVGPDGLM M NP_009057 Valosin containing protein A VEFKVVETD D Q99622 Homeobox C10 protein A QDPE I ASL L NP_055531 Centaurin b1 K LDSHAEL L L P61604 HSP10 G DILGKYVD D P41091 eIF2G R QDLTTLDV V CAA50726 Topoisomerase IIb G LDKDEYTF F EAX04806 Hypot het ical prot ein FLJ20035 S VG IGPARF F Q8TBE7 Transmembrane protein TMEM22 A LDKFHPAL L P20073 Annexin A7 G QYPYPSGF F EAW69005 CD23 G QYSE I EEL L P46695 Radiation-inducible gene product PRG1 G QHGLEEDFM M P52630 Transcription factor STAT2 S QDPESLLL L Q13614 Myotubularin related protein 2 R QFPTAFEF F Q9P2D0 Inhibitor of Burton tyrosine kinase A LNRE I LFV V Q15274 Quinolinate phosphoribosyl transferase A LDFSLKL L O95336 6-phosphogluconolactonase S LFPDHPL L L O60287 Nuclear preribosomal-associated protein 1 V LDQKI LLL L EAW53437 POGZ protein R QFSTPFQL L NP_036465 C-myc binding protein G MDVAASEFF F P15498 Protooncogene Vav K MDRYAFLL L P30043 Flavin reductase G QDAV I VLL L NP_11558 Nucleotide-binding oligomerization domain 27 R LDLSHLLL L AAS75801 Phosphoinositide-3 kinase, gamma polypeptide R QDML I LQ I I AAH03099 DPH1 protein A QDFRVLYV V Supplemental figure S3

1 90 | a1 | Patr-AL EAL-2 GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASKRMEPRAP WMEQEE PEYW DQETQISKVY AQNDRVNLGT LRGYYNQSEA Patr-AL EAL-1 ...... Patr-AL FRAL-1 ...... I...... HLA-A*0201 ...... Q...... I...G.... .G..RKV.AH S.TH..D...... HLA-A*0207 ...... Q...... I...G.... .G..RKV.AH S.TH..D......

91 180 | a2 | Patr-AL EAL-2 GSHTIQLMYG CDVGPDGRFL RGYRQYAYDG KDYIALNED L RSWTAADMAA RITKRKWEAA RRAEQLRVYL KGRCVDWLRR YVENGKEMLQ Patr-AL EAL-1 D...... Patr-AL FRAL-1 ...... HLA-A*0201 ....V.R...... S.W...... H...... K...... QT..H..... HV.....A.. E.T..E.... .L.....T.. HLA-A*0207 ....V.R.C. ....S.W...... H...... K...... QT..H..... HV.....A.. E.T..E.... .L.....T..

181 2 70 | a3 | Patr-AL EAL-2 RTDAPKTRM THH PVSDRETTL RCWALGFYP AEITLTWQRD GEDQTQDTELV ETRPAGDGT FQKWAAVVVPS GKEQRYTCL VQHEGLPEPL Patr-AL EAL-1 ...... Patr-AL FRAL-1 ...... HLA-A*0201 ...... H. ... A...H.A...... S...... Q...... H ...... K.. HLA-A*0207 ...... H. ... A...H.A...... S...... Q...... H ...... K..

281 3 41 | Stem | Transmembrane | Cytoplasmic | Patr-AL EAL-2 TLRWEPSSQP TIPIVGIIAG LV LFVAVI TG AVV AA VM WRR KSSDRKGGSY FQAA SNDSSQ GSEVSLTACKV Patr-AL EAL-1 ...... Patr-AL FRAL-1 ...... HLA-A*0201 ...... G...... S... .S ..A. ..D...... HLA-A*0207 ...... G...... S... .S ..A. ..D...... Supplemental figure S4

A5T6 A5 T6 K4L8 K4 L8

N3V7 N3 V7

A1L2L9 A1 L2 L9 Supplemental figure S5

A*2402 VYGFVRACL A*1101 KTFPPTEPK A*1101 AIFQSSMTK B*0801 FLRGRAYGL G*0101 RIIPRHLQL Patr-AL C*0301 GAVDPLLAL B*1501 ILGPPGSVY vs E*0101 VMAPRTVLL B*3501 KPIVVLHGY non-A*02 B*2705 RRRWHRWRL C*0401 QYDDAVYKL B*5301 KPIVQYDNF A*0101 EADPTGHSY B*4403 EEPTVIKKY B*4401 EEFGRAFSF *** Patr-AL A*0201 ILKEPVHGV A*0201 TLTSCNTSV vs A*0201 GILGFVFTL A*0201 ALWGFFPVL A*0201 A*0201 FLWGPRALV A*0201 LLFGYPVYV

ILKEPVHGV vs. TLTSCNTSV FLWGPRALV vs. TLTSCNTSV TLTSCNTSV vs. ALWGFFPVL ns GILGFVFTL vs. TLTSCNTSV ILKEPVHGV vs. LLFGYPVYV A*0201 TLTSCNTSV vs. LLFGYPVYV FLWGPRALV vs. GILGFVFTL vs FLWGPRALV vs. ILKEPVHGV ILKEPVHGV vs. ALWGFFPVL A*0201 GILGFVFTL vs. LLFGYPVYV LLFGYPVYV vs. ALWGFFPVL FLWGPRALV vs. ALWGFFPVL GILGFVFTL vs. ALWGFFPVL GILGFVFTL vs. ILKEPVHGV FLWGPRALV vs. LLFGYPVYV 0.5 1 1.5 2 2.5 RMSD, Å Supplemental figure S6

Gogo*A0401 A*6801 A*6802 72 A*2601 / A*6601 55* A*3401 Patr-A*0302 A*0101 /A*0103 A*0301 / A*0302 0.01 A*1101 A*3303 A*3101 A*3201 A*2902 Patr-A*0901 Patr-A*0401 Patr-A*0701 A*2301 / A*2402 A*0201 / A*0207 Patr-AL 83 Gogo-A*0501 61 HLA-Y * Popy-A*05 * 50 Popy-A*04 73 Popy-A*02 Popy-A*03 Mamu-AG4 84 * Mamu-AG2 81 Mamu-AG3 Mamu-A3 Mamu-A1 Mamu-A2